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Chang C, Banerjee SL, Park SS, Zhang XL, Cotnoir-White D, Opperman KJ, Desbois M, Grill B, Kania A. Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function. eLife 2024; 12:RP89176. [PMID: 38289221 PMCID: PMC10945567 DOI: 10.7554/elife.89176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Eph receptor tyrosine kinases participate in a variety of normal and pathogenic processes during development and throughout adulthood. This versatility is likely facilitated by the ability of Eph receptors to signal through diverse cellular signalling pathways: primarily by controlling cytoskeletal dynamics, but also by regulating cellular growth, proliferation, and survival. Despite many proteins linked to these signalling pathways interacting with Eph receptors, the specific mechanisms behind such links and their coordination remain to be elucidated. In a proteomics screen for novel EPHB2 multi-effector proteins, we identified human MYC binding protein 2 (MYCBP2 or PAM or Phr1). MYCBP2 is a large signalling hub involved in diverse processes such as neuronal connectivity, synaptic growth, cell division, neuronal survival, and protein ubiquitination. Our biochemical experiments demonstrate that the formation of a complex containing EPHB2 and MYCBP2 is facilitated by FBXO45, a protein known to select substrates for MYCBP2 ubiquitin ligase activity. Formation of the MYCBP2-EPHB2 complex does not require EPHB2 tyrosine kinase activity and is destabilised by binding of ephrin-B ligands, suggesting that the MYCBP2-EPHB2 association is a prelude to EPHB2 signalling. Paradoxically, the loss of MYCBP2 results in increased ubiquitination of EPHB2 and a decrease of its protein levels suggesting that MYCBP2 stabilises EPHB2. Commensurate with this effect, our cellular experiments reveal that MYCBP2 is essential for efficient EPHB2 signalling responses in cell lines and primary neurons. Finally, our genetic studies in Caenorhabditis elegans provide in vivo evidence that the ephrin receptor VAB-1 displays genetic interactions with known MYCBP2 binding proteins. Together, our results align with the similarity of neurodevelopmental phenotypes caused by MYCBP2 and EPHB2 loss of function, and couple EPHB2 to a signalling effector that controls diverse cellular functions.
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Affiliation(s)
- Chao Chang
- Institut de recherches cliniques de Montréal (IRCM)MontréalCanada
- Integrated Program in Neuroscience, McGill UniversityMontréalCanada
| | - Sara L Banerjee
- Institut de recherches cliniques de Montréal (IRCM)MontréalCanada
- Division of Experimental Medicine, McGill UniversityMontréalCanada
| | - Sung Soon Park
- Institut de recherches cliniques de Montréal (IRCM)MontréalCanada
- Integrated Program in Neuroscience, McGill UniversityMontréalCanada
| | - Xiao Lei Zhang
- Institut de recherches cliniques de Montréal (IRCM)MontréalCanada
| | | | - Karla J Opperman
- Center for Integrative Brain Research, Seattle Children’s Research InstituteSeattleUnited States
| | - Muriel Desbois
- Center for Integrative Brain Research, Seattle Children’s Research InstituteSeattleUnited States
- School of Life Sciences, Keele UniversityKeeleUnited Kingdom
| | - Brock Grill
- Center for Integrative Brain Research, Seattle Children’s Research InstituteSeattleUnited States
- Department of Pediatrics, University of Washington School of MedicineSeattleUnited States
- Department of Pharmacology, University of Washington School of MedicineSeattleUnited States
| | - Artur Kania
- Institut de recherches cliniques de Montréal (IRCM)MontréalCanada
- Integrated Program in Neuroscience, McGill UniversityMontréalCanada
- Division of Experimental Medicine, McGill UniversityMontréalCanada
- Department of Anatomy and Cell Biology, McGill UniversityMontréalCanada
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Amezquita J, Desbois M, Opperman KJ, Pak JS, Christensen EL, Nguyen NT, Diaz-Garcia K, Borgen MA, Grill B. Axon development is regulated at genetic and proteomic interfaces between the integrin adhesome and the RPM-1 ubiquitin ligase signaling hub. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.566604. [PMID: 38014183 PMCID: PMC10680716 DOI: 10.1101/2023.11.15.566604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Integrin signaling plays important roles in development and disease. An adhesion signaling network called the integrin adhesome has been principally defined using bioinformatics and proteomics. To date, the adhesome has not been studied using integrated proteomic and genetic approaches. Here, proteomic studies in C. elegans identified physical associations between the RPM-1 ubiquitin ligase signaling hub and numerous adhesome components including Talin, Kindlin and beta-integrin. C. elegans RPM-1 is orthologous to human MYCBP2, a prominent player in nervous system development associated with a neurodevelopmental disorder. Using neuron-specific, CRISPR loss-of-function strategies, we show that core adhesome components affect axon development and interact genetically with RPM-1. Mechanistically, Talin opposes RPM-1 in a functional 'tug-of-war' on growth cones that is required for accurate axon termination. Thus, our findings orthogonally validate the adhesome via multi-component genetic and physical interfaces with a key neuronal signaling hub and identify new links between the adhesome and brain disorders.
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Chang C, Banerjee SL, Park SS, Zhang X, Cotnoir-White D, Opperman KJ, Desbois M, Grill B, Kania A. Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544638. [PMID: 37693478 PMCID: PMC10491099 DOI: 10.1101/2023.06.12.544638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Eph receptor tyrosine kinases participate in a variety of normal and pathogenic processes during development and throughout adulthood. This versatility is likely facilitated by the ability of Eph receptors to signal through diverse cellular signalling pathways: primarily by controlling cytoskeletal dynamics, but also by regulating cellular growth, proliferation, and survival. Despite many proteins linked to these signalling pathways interacting with Eph receptors, the specific mechanisms behind such links and their coordination remain to be elucidated. In a proteomics screen for novel EPHB2 multi-effector proteins, we identified human MYC binding protein 2 (MYCBP2 or PAM or Phr1). MYCBP2 is a large signalling hub involved in diverse processes such as neuronal connectivity, synaptic growth, cell division, neuronal survival, and protein ubiquitination. Our biochemical experiments demonstrate that the formation of a complex containing EPHB2 and MYCBP2 is facilitated by FBXO45, a protein known to select substrates for MYCBP2 ubiquitin ligase activity. Formation of the MYCBP2-EPHB2 complex does not require EPHB2 tyrosine kinase activity and is destabilised by binding of ephrin-B ligands, suggesting that the MYCBP2-EPHB2 association is a prelude to EPHB2 signalling. Paradoxically, the loss of MYCBP2 results in increased ubiquitination of EPHB2 and a decrease of its protein levels suggesting that MYCBP2 stabilises EPHB2. Commensurate with this effect, our cellular experiments reveal that MYCBP2 is essential for efficient EPHB2 signalling responses in cell lines and primary neurons. Finally, our genetic studies in C. elegans provide in vivo evidence that the ephrin receptor VAB-1 displays genetic interactions with known MYCBP2 binding proteins. Together, our results align with the similarity of neurodevelopmental phenotypes caused by MYCBP2 and EPHB2 loss of function, and couple EPHB2 to a signaling effector that controls diverse cellular functions.
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Affiliation(s)
- Chao Chang
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Sara L. Banerjee
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, H3A 2B2, Canada
| | - Sung Soon Park
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Xiaolei Zhang
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
| | - David Cotnoir-White
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
| | - Karla J. Opperman
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Muriel Desbois
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- School of Life Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Brock Grill
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Artur Kania
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, QC, H3A 2B4, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, H3A 2B2, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
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Desbois M, Pak JS, Opperman KJ, Giles AC, Grill B. Optimized protocol for in vivo affinity purification proteomics and biochemistry using C. elegans. STAR Protoc 2023; 4:102262. [PMID: 37294631 PMCID: PMC10323129 DOI: 10.1016/j.xpro.2023.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 06/11/2023] Open
Abstract
We present an optimized protocol for in vivo affinity purification proteomics and biochemistry using the model organism C. elegans. We describe steps for target tagging, large-scale culture, affinity purification using a cryomill, mass spectrometry and validation of candidate binding proteins. Our approach has proven successful for identifying protein-protein interactions and signaling networks with verified functional relevance. Our protocol is also suitable for biochemical evaluation of protein-protein interactions in vivo. For complete details on the use and execution of this protocol, please refer to Crawley et al.,1 Giles et al.,2 and Desbois et al.3.
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Affiliation(s)
- Muriel Desbois
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Joseph S Pak
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karla J Opperman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Andrew C Giles
- Division of Medical Sciences, University of Northern British Columbia, Prince George, BC V2N 4Z9 Canada
| | - Brock Grill
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington Medical School, Seattle, WA 98101, USA; Department of Pharmacology, University of Washington Medical School, Seattle, WA 98101, USA.
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5
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AlAbdi L, Desbois M, Rusnac DV, Sulaiman RA, Rosenfeld JA, Lalani S, Murdock DR, Burrage LC, Billie Au PY, Towner S, Wilson WG, Wong L, Brunet T, Strobl-Wildemann G, Burton JE, Hoganson G, McWalter K, Begtrup A, Zarate YA, Christensen EL, Opperman KJ, Giles AC, Helaby R, Kania A, Zheng N, Grill B, Alkuraya FS. Loss-of-function variants in MYCBP2 cause neurobehavioural phenotypes and corpus callosum defects. Brain 2023; 146:1373-1387. [PMID: 36200388 PMCID: PMC10319777 DOI: 10.1093/brain/awac364] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 11/14/2022] Open
Abstract
The corpus callosum is a bundle of axon fibres that connects the two hemispheres of the brain. Neurodevelopmental disorders that feature dysgenesis of the corpus callosum as a core phenotype offer a valuable window into pathology derived from abnormal axon development. Here, we describe a cohort of eight patients with a neurodevelopmental disorder characterized by a range of deficits including corpus callosum abnormalities, developmental delay, intellectual disability, epilepsy and autistic features. Each patient harboured a distinct de novo variant in MYCBP2, a gene encoding an atypical really interesting new gene (RING) ubiquitin ligase and signalling hub with evolutionarily conserved functions in axon development. We used CRISPR/Cas9 gene editing to introduce disease-associated variants into conserved residues in the Caenorhabditis elegans MYCBP2 orthologue, RPM-1, and evaluated functional outcomes in vivo. Consistent with variable phenotypes in patients with MYCBP2 variants, C. elegans carrying the corresponding human mutations in rpm-1 displayed axonal and behavioural abnormalities including altered habituation. Furthermore, abnormal axonal accumulation of the autophagy marker LGG-1/LC3 occurred in variants that affect RPM-1 ubiquitin ligase activity. Functional genetic outcomes from anatomical, cell biological and behavioural readouts indicate that MYCBP2 variants are likely to result in loss of function. Collectively, our results from multiple human patients and CRISPR gene editing with an in vivo animal model support a direct link between MYCBP2 and a human neurodevelopmental spectrum disorder that we term, MYCBP2-related developmental delay with corpus callosum defects (MDCD).
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh 11362, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Muriel Desbois
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Domniţa-Valeria Rusnac
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Raashda A Sulaiman
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Ping Yee Billie Au
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Shelley Towner
- Pediatric Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - William G Wilson
- Pediatric Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lawrence Wong
- Department of Genetics, Northern California Kaiser Permanente, Oakland, CA 94611, USA
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics (ING), Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Jennifer E Burton
- Department of Genetics, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
| | - George Hoganson
- Department of Genetics, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
| | - Kirsty McWalter
- Genedx, Inc., 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Amber Begtrup
- Genedx, Inc., 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Elyse L Christensen
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Karla J Opperman
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Andrew C Giles
- Division of Medical Sciences, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Artur Kania
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, QC H3A 2B4, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC H3A 2B2, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
| | - Ning Zheng
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Brock Grill
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
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Squair DR, Virdee S. A new dawn beyond lysine ubiquitination. Nat Chem Biol 2022; 18:802-811. [PMID: 35896829 DOI: 10.1038/s41589-022-01088-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/21/2022] [Indexed: 01/18/2023]
Abstract
The ubiquitin system has become synonymous with the modification of lysine residues. However, the substrate scope and diversity of the conjugation machinery have been underappreciated, bringing us to an epoch in ubiquitin system research. The striking discoveries of metazoan enzymes dedicated toward serine and threonine ubiquitination have revealed the important role of nonlysine ubiquitination in endoplasmic reticulum-associated degradation, immune signaling and neuronal processes, while reports of nonproteinaceous substrates have extended ubiquitination beyond the proteome. Bacterial effectors that bypass the canonical ubiquitination machinery and form unprecedented linkage chemistry further redefine long-standing dogma. While chemical biology approaches have advanced our understanding of the canonical ubiquitin system, further study of noncanonical ubiquitination has been hampered by a lack of suitable tools. This Perspective aims to consolidate and contextualize recent discoveries and to propose potential applications of chemical biology, which will be instrumental in unraveling this new frontier of ubiquitin research.
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Affiliation(s)
- Daniel R Squair
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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